Update from the nf-core/cellpainting developer meeting today Attendees: @Josh Shapiro @Dave Bunten @Florian Wuennemann • Template update merged into

dev

. Thanks to @mashehu for getting all checks green. The older template PR was also closed by Matthias, we are on the latest template now! • CytoTable / pycytominer PRs (from Riley, Ken and Jillian): Dave will review them against recent CytoTable and pycytominer changes. Where rebasing is too messy, he’ll consolidate them into a fresh branch on the nf-core repo, credit the original authors as co-authors, and then ping for review and merge. • Design note: @Josh Shapiro pointed out, we shouldn’t assume a single plate map per run. Multi-plate runs will often have several plate maps, and users shouldn’t need to rerun the workflow to handle them. • Downstream analysis: Josh shared his pipeline for feature selection, grouping plates or samples, and UMAPs (github.com/AlexsLemonade/morphport). It could be chained downstream of nf-core/cellpainting as a meta-pipeline. One open problem: CytoTable presets often don’t fit Cell Painting Gallery datasets. Ideas raised were a YAML/JSON join spec and Dave’s LinkML-based dataset descriptions. • Next goal: get the pipeline running end to end and reproduce results on a Cell Painting Gallery dataset. 🙋 We’re looking for testers with real data. Next meeting in about a month.